The Stanford Cancer Genome Characterization Center (CGCC) will capitalize on established strengths in high-throughput genome analysis and unique technological expertise and will carry out systematic, genome-wide analysis on DNA methylation and DNA copy number changes in human cancers. The Stanford CGCC will join a consortium of Cancer Genome Centers with the broad goals of carrying out detailed genome analysis of the genetic, epigenetic and gene expression changes in human cancers and correlating these changes with clinical, pathological and outcome data to gain insights into cancer biology, improve cancer classification and diagnosis, and identify new molecular targets and strategies for treatment. The Stanford CGCC is a multidisciplinary group with expertise in high-throughput genome analysis, bioinformatics, genetics, cancer biology and clinical cancer care. Using high quality DNAs obtained from matched normal and malignant tissues provided by the Human Cancer Biospecimen Core Resource of The Cancer Genome Atlas Project, the Stanford CGCC proposes to: 1) characterize comprehensive DNA methylation changes at CpG Islands and other CpG-rich regions of the human genome in normal and malignant tissues by using a new microarray based technology, and 2) identify genome-wide changes in DNA copy number in normal and malignant tissues. Data generated and tools developed will be made available rapidly without restriction to the CGCC groups and scientific community. Clinical and biological significance of the data will be identified by correlating copy number and methylation changes with gene expression and clinical outcome data available through the CGCC consortium.